antonkulaga created TOREE-478:
---------------------------------
Summary: Problems with dependencies
Key: TOREE-478
URL: https://issues.apache.org/jira/browse/TOREE-478
Project: TOREE
Issue Type: Bug
Affects Versions: 0.2.0
Environment: Linux Mint, docker container based on latest
jupyter/all-spark-notebook
https://github.com/antonkulaga/bigdata-docker/blob/master/containers/spark-ml-notebook/Dockerfile
Reporter: antonkulaga
Whenever I try to import some libs, like:
%AddDeps org.bdgenomics.adam adam-core-spark2_2.11 0.24.0 --transitive
%AddDeps comp.bio.aging adam-playground_2.11 0.0.13 --repository
https://dl.bintray.com/comp-bio-aging/main/
And then start using them in a cell:
import org.bdgenomics.adam.rdd.ADAMContext._
val genage = sc.loadFasta("/path/to/my/fasta/file"))
I get:
lastException = null
Name: org.apache.spark.SparkException
Message: Job aborted due to stage failure: ClassNotFound with classloader:
scala.reflect.internal.util.ScalaClassLoader$URLClassLoader@4c2a056b
StackTrace: at
org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1590)
at
org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1589)
at
scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1589)
at
org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:831)
at
org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:831)
at scala.Option.foreach(Option.scala:257)
at
org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:831)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1823)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1772)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1761)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:642)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2034)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2055)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2074)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2099)
at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:939)
at
org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at
org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
at org.apache.spark.rdd.RDD.withScope(RDD.scala:363)
at org.apache.spark.rdd.RDD.collect(RDD.scala:938)
at
org.bdgenomics.adam.rdd.contig.NucleotideContigFragmentRDD$.apply(NucleotideContigFragmentRDD.scala:95)
at
org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadFasta$1.apply(ADAMContext.scala:2488)
at
org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadFasta$1.apply(ADAMContext.scala:2472)
at scala.Option.fold(Option.scala:158)
at org.apache.spark.rdd.Timer.time(Timer.scala:48)
at org.bdgenomics.adam.rdd.ADAMContext.loadFasta(ADAMContext.scala:2472)
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